Circle size represents number of papers published per research area; the
number of publications per discipline
given below the map. The knowledge
input (such as in terms of read or cited
papers) and output (such as in terms
of published or funded papers) of an
individual, institution, or country can
be mapped to indicate core competen-cies. Most publication output of the
four network-science researchers is in
physics.
These and many other Sci2 analyses
and corresponding visualizations are
highly scalable; thousands of authors,
references, and projects can be viewed
simultaneously, and visualizations can
be saved in vector format for further
manipulation.
Macroscope synergies
Just as the value of the earliest telephones increased in proportion to
the number of people using them,
plug-and-play macroscopes gain value
relative to the increase in their core
functionality; numbers of data-set and
algorithm plug-ins; and the researchers, educators, and practitioners using
and advancing them.
OSGi/CIShell-compliant plug-ins
can be shared among tools and projects; for example, network-analysis
algorithms implemented for the NWB
tool can be shared as Java Archive files
through email or other means, saved
in the plug-in directory of another
tool, and made available for execution in the menu system of that tool.
Text-mining algorithms originally developed in TEXTrend (discussed later)
can be plugged into the Sci2 tool to
support semantic analysis of scholarly
texts. Though National Science Foundation funding for the NWB tool formally ended in 2009, NWB’s functionality continues to increase, as plug-ins
developed for other tools become
available. Even if no project or agency
were to fund the OSGi/CIShell core for
some time, it would remain functional, due to it being lightweight and easy
to maintain. Finally, the true value of
OSGi/CIShell is due to the continuously evolving algorithm filling and
the “custom tools” continuously developed and shared by domain scientists.
Over the past five years, a number of
projects have adopted OSGi (and in two
cases, CIShell):
as the functionality
of osGi/cishell-
based software
frameworks
improves, and as
the number and
diversity of data-set
and algorithm
plug-ins increases,
so too will the
capabilities
of custom
macroscopes.
˲ ˲ Cytoscape ( http://cytoscape.org).
Led by Trey Ideker at the University of California, San Diego, this
open-source bioinformatics software platform enables visualization
of molecular-interaction networks,
gene-expression profiles, and other
state data. 15 Inspired by a workshop on
software infrastructures in July 2007
( https://nwb.slis.indiana.edu/events/
ivsi2007), Mike Smoot and Bruce W.
Herr implemented a proof-of-concept
OSGi-based Cytoscape core several
months later; OSGi bundles are available at http://chianti.ucsd.edu/svn/
core3. Once the new Cytoscape 3.0
core is implemented (projected mid-
2011), sharing plug-ins between the
NWB tool and Cytoscape will be much
easier, thereby extending the functionality and utility of both;
˲ ˲ Taverna Workbench (
http://taver-na.org.uk). Developed by the myGrid
team ( http://mygrid.org.uk) led by
Carol Goble at the University of Manchester, U.K., this suite of free open-source software tools helps design and
execute workflows, 12 allowing users
to integrate many different software
tools, including more than 8,000 Web
services from diverse domains, including chemistry, music, and social
sciences. The workflows are designed
in the Taverna Workbench and can
then be run on a Taverna Engine, in
the Workbench, on an external server,
in a portal, on a computational grid,
or on a compute cloud. Raven (a Tav-erna-specific classloader and registry
mechanism) supports an extensible
and flexible architecture (with approximately 20 plug-ins) but an implementation using an OSGi framework,
with alpha release was scheduled for
February 2011. The myExperiment
( http://myexperiment.org) social Web
site supports the finding and sharing
of workflows and provides special support for Taverna workflows9;
˲ ˲ MAEviz ( https://wiki.ncsa.uiuc.
edu/display/MAE/Home). Managed by
Shawn Hampton of the National Center
for Supercomputing Applications, this
open-source, extensible software platform supports seismic risk assessment
based on Mid-America Earthquake
Center research in the Consequence-Based Risk Management framework. 10
It also uses the Eclipse Rich Client
Platform, including Equinox, a com-